GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_01112 in Sinorhizobium meliloti 1021

Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate SMc03814 SMc03814 ABC transporter permease

Query= reanno::Burk376:H281DRAFT_01112
         (364 letters)



>FitnessBrowser__Smeli:SMc03814
          Length = 335

 Score =  157 bits (396), Expect = 5e-43
 Identities = 102/313 (32%), Positives = 158/313 (50%), Gaps = 11/313 (3%)

Query: 52  WFTVALIVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGIDVSFTAI 111
           W  +A++V+  L+V  I+ +F     L ++  +A  + + ALG   VL SGGID+S  +I
Sbjct: 33  WIALAILVIG-LVVSVISAKFATSGNLLNIFQNACFIGIMALGMTPVLISGGIDISVGSI 91

Query: 112 AALTMYGITKAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIVTIGTQYL 171
             L M G+T  +     D P A+ ++     GV  GMVNG+++  +K P  IVT+ T  +
Sbjct: 92  --LGMCGVTLGIVLN-SDMPLAVGILATLAMGVACGMVNGIIISYVKLPPFIVTLATLSI 148

Query: 172 YRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAAVVTWWLL 231
            R L L       F         FGR          G    LP  V ALVA  ++  +LL
Sbjct: 149 GRSLALVLTNNEVFYE-------FGRATNGIIALGGGYSFGLPNVVYALVAGVIILHFLL 201

Query: 232 NRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRLANPFDL 291
             T  GR ++A+GG+ A A   G  +  I +  + + G++  I  +  V           
Sbjct: 202 TMTRWGRYLFAIGGNEAAARLAGIPVDLIKVSAYAFNGLMVAITAVFLVGWLGAVTNAIG 261

Query: 292 VGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQKVIIGAFI 351
            G EL VIA+ ++GGA +TGG GT +G  +G +LV +I++ L++ GV   WQ + +G+FI
Sbjct: 262 TGYELQVIASTVIGGASLTGGFGTALGAAIGAILVEVIRNALLIAGVNPFWQGMFVGSFI 321

Query: 352 LLAGTLFALQRKR 364
           L A  L  ++  R
Sbjct: 322 LAAVLLERIRSLR 334


Lambda     K      H
   0.328    0.141    0.426 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 295
Number of extensions: 18
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 364
Length of database: 335
Length adjustment: 29
Effective length of query: 335
Effective length of database: 306
Effective search space:   102510
Effective search space used:   102510
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory